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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/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' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $species_info = array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ) $local_species = 'sci' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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 45 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ), 'gf_id' => 'HOM05D001139', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001139' ), 'data_identifier' => 'HOM05D001139', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001139', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '543', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p31860' => 'bna', 'A02p10100' => 'bna', 'A03p14490' => 'bna', 'A04p07640' => 'bna', 'A05p19770' => 'bna', 'A07p09270' => 'bna', 'A10p11970' => 'bna', 'Aa31LG10G3390' => 'aar', 'Aa31LG3G10610' => 'aar', 'Aa31LG5G10260' => 'aar', 'Aa31LG8G9710' => 'aar', 'Aa31LG9G2910' => 'aar', 'Aa31LG9G2920' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3206' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.527' => 'aag', 'Actinidia04455' => 'ach', 'Actinidia05126' => 'ach', 'Actinidia09958' => 'ach', 'Actinidia10704' => 'ach', 'Actinidia11340' => 'ach', 'Actinidia12492' => 'ach', 'Actinidia35313' => 'ach', 'Actinidia39893' => 'ach', 'Actinidia40062' => 'ach', 'Ah.04g156080' => 'amhyb', 'Ah.06g183100' => 'amhyb', 'Ah.09g237170' => 'amhyb', 'Ah.13g072430' => 'amhyb', 'AL1G58870' => 'aly', 'AL307U10010' => 'aly', 'AL3G37860' => 'aly', 'AL7G41760' => 'aly', 'AL7G41790' => 'aly', 'AL8G30130' => 'aly', 'Aqoxy4G02124' => 'aox', 'Aqoxy5G00254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.11KZZ9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.2TQQ6M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.38ENMU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7X0NJW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.AJV249' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DY6X0K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UF0TAZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YHH73E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z4TF31' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZSV3DU' => 'arhy', 'AT1G51070' => 'ath', 'AT3G23210' => 'ath', 'AT4G14410' => 'ath', 'AT5G54680' => 'ath', 'ATR0618G005' => 'atr', 'ATR0680G338' => 'atr', 'ATR1088G025' => 'atr', 'Atru.chr10.2107' => 'acertr', 'Atru.chr10.2109' => 'acertr', 'Atru.chr2.3184' => 'acertr', 'Atru.chr2.3194' => 'acertr', 'Atru.chr4.2092' => 'acertr', 'Atru.chr6.3130' => 'acertr', 'AUR62002110' => 'cqu', 'AUR62012588' => 'cqu', 'AUR62014614' => 'cqu', 'AUR62015636' => 'cqu', 'AUR62028228' => 'cqu', 'AUR62029235' => 'cqu', 'AUR62034025' => 'cqu', 'AUR62036847' => 'cqu', 'AUR62042938' => 'cqu', 'BcaB01g04310' => 'bca', 'BcaB02g08610' => 'bca', 'BcaB02g11210' => 'bca', 'BcaB03g12522' => 'bca', 'BcaB03g16653' => 'bca', 'BcaB04g20464' => 'bca', 'BcaB05g22154' => 'bca', 'BcaB06g26456' => 'bca', 'BcaB08g35829' => 'bca', 'BcaC01g06318' => 'bca', 'BcaC02g09315' => 'bca', 'BcaC03g14297' => 'bca', 'BcaC04g20312' => 'bca', 'BcaC05g27373' => 'bca', 'BcaC09g49262' => 'bca', 'BolC1t04033H' => 'bol', 'BolC2t07780H' => 'bol', 'BolC3t14106H' => 'bol', 'BolC4t25709H' => 'bol', 'BolC5t32029H' => 'bol', 'BolC7t41925H' => 'bol', 'BolC7t41928H' => 'bol', 'BolC9t57383H' => 'bol', 'BraA01t03312Z' => 'bra', 'BraA02t06079Z' => 'bra', 'BraA03t10744Z' => 'bra', 'BraA04t16455Z' => 'bra', 'BraA05t20884Z' => 'bra', 'BraA07t28726Z' => 'bra', 'BraA10t43293Z' => 'bra', 'C01p40750' => 'bna', 'C02p16750' => 'bna', 'C03p16920' => 'bna', 'C04p41310' => 'bna', 'C05p33020' => 'bna', 'C07p14320' => 'bna', 'C07p14330' => 'bna', 'C09p45080' => 'bna', 'CAN.G1110.12' => 'can', 'CAN.G1587.4' => 'can', 'CAN.G337.154' => 'can', 'CAN.G569.61' => 'can', 'CAN.G793.34' => 'can', 'CANSAT11G2613' => 'cansat', 'CANSAT56G3338' => 'cansat', 'CANSAT64G1330' => 'cansat', 'CANSAT78G2443' => 'cansat', 'CARHR041090' => 'chi', 'CARHR099160' => 'chi', 'CARHR220620' => 'chi', 'CARHR267990' => 'chi', 'Carub.0001s3997' => 'cru', 'Carub.0003s2344' => 'cru', 'Carub.0007s2781' => 'cru', 'Carub.0008s1494' => 'cru', 'Ca_01570_v3' => 'car', 'Ca_01758_v3' => 'car', 'Ca_01764_v3' => 'car', 'Ca_11965_v3' => 'car', 'CBR_g36820' => 'cbr', 'CBR_g58807' => 'cbr', 'Cc02_g11750' => 'ccan', 'Cc03_g05370' => 'ccan', 'Cc05_g13180' => 'ccan', 'CDE01G0163' => 'cde', 'CDE02G0699' => 'cde', 'CDE04G0990' => 'cde', 'CDE04G1465' => 'cde', 'CDE04G1631' => 'cde', 'CDE05G1103' => 'cde', 'CDE08G0061' => 'cde', 'CDE12G0594' => 'cde', 'Cfa008327' => 'cfa', 'Cfa016412' => 'cfa', 'Cfa020434' => 'cfa', 'Ciclev10005872m.g' => 'ccl', 'Ciclev10009354m.g' => 'ccl', 'Ciclev10016381m.g' => 'ccl', 'Ciclev10016511m.g' => 'ccl', 'CiPaw.01G186700' => 'cil', 'CiPaw.02G113900' => 'cil', 'CiPaw.03G163600' => 'cil', 'CiPaw.09G080700' => 'cil', 'CiPaw.11G183100' => 'cil', 'CiPaw.12G126000' => 'cil', 'ClCG02G008370' => 'cla', 'ClCG03G005100' => 'cla', 'ClCG05G014800' => 'cla', 'ClCG10G005740' => 'cla', 'COL.COLO4_09558' => 'col', 'COL.COLO4_13001' => 'col', 'COL.COLO4_31689' => 'col', 'Cpa.g.c33751' => 'cpa', 'Cpa.g.sc44.78' => 'cpa', 'Cpa.g.sc81.11' => 'cpa', 'Cpa.g.sc97.78' => 'cpa', 'Cre05.g241636' => 'cre', 'CsaV3_1G011300' => 'csa', 'CsaV3_2G035250' => 'csa', 'CsaV3_3G012210' => 'csa', 'CsaV3_3G022870' => 'csa', 'CsaV3_3G022920' => 'csa', 'CsaV3_3G022930' => 'csa', 'CsaV3_UNG229040' => 'csa', 'CSS0001584' => 'camsi', 'CSS0003058' => 'camsi', 'CSS0022204' => 'camsi', 'CSS0023261' => 'camsi', 'CSS0025308' => 'camsi', 'CSS0028637' => 'camsi', 'CSS0031082' => 'camsi', 'DCAR_004176' => 'dca', 'DCAR_004178' => 'dca', 'DCAR_008114' => 'dca', 'DCAR_010015' => 'dca', 'DCAR_019207' => 'dca', 'DCAR_021193' => 'dca', 'DCAR_022520' => 'dca', 'DCAR_024243' => 'dca', 'Dinv10910' => 'din', 'Dinv17846' => 'din', 'Dinv18538' => 'din', 'Dinv18924' => 'din', 'Dinv22312' => 'din', 'Dinv27037' => 'din', 'Duzib052G0005' => 'dzi', 'Duzib052G0240' => 'dzi', 'Duzib151G0978' => 'dzi', 'Duzib170G0527' => 'dzi', 'Duzib213G0055' => 'dzi', 'Duzib235G0873' => 'dzi', 'Duzib268G0151' => 'dzi', 'ECA233G3115' => 'eca', 'ECA236G1853' => 'eca', 'ECA240G2654' => 'eca', 'ECA246G5045' => 'eca', 'EL10Ac3g05030' => 'bvu', 'EL10Ac4g07986' => 'bvu', 'EL10Ac4g09217' => 'bvu', 'Eucgr.F03420' => 'egr', 'Eucgr.H00174' => 'egr', 'Eucgr.K00871' => 'egr', 'FAN11G2186' => 'fan', 'FAN12G2721' => 'fan', 'FAN16G3065' => 'fan', 'FAN17G1458' => 'fan', 'FAN21G0033' => 'fan', 'FAN22G0574' => 'fan', 'FAN25G0134' => 'fan', 'FAN25G1929' => 'fan', 'FAN25G2393' => 'fan', 'FAN25G2588' => 'fan', 'FvH4_3g02910' => 'fve', 'FvH4_3g21720' => 'fve', 'FvH4_4g03420' => 'fve', 'Glyma.06G266800' => 'gma', 'Glyma.10G007300' => 'gma', 'Glyma.12G136300' => 'gma', 'Glyma.12G196700' => 'gma', 'Glyma.12G214900' => 'gma', 'Glyma.13G251300' => 'gma', 'Glyma.13G286700' => 'gma', 'Glyma.13G305500' => 'gma', 'Glyma.15G062600' => 'gma', 'Glyma.15G063000' => 'gma', 'Glyma.20G088600' => 'gma', 'Gohir.A01G013500' => 'ghi', 'Gohir.A01G074000' => 'ghi', 'Gohir.A05G167800' => 'ghi', 'Gohir.A10G112800' => 'ghi', 'Gohir.A11G280600' => 'ghi', 'Gohir.A13G141600' => 'ghi', 'Gohir.D01G014800' => 'ghi', 'Gohir.D01G060500' => 'ghi', 'Gohir.D05G170800' => 'ghi', 'Gohir.D10G154600' => 'ghi', 'Gohir.D11G290900' => 'ghi', 'Gohir.D13G146300' => 'ghi', 'Gorai.002G016500' => 'gra', 'Gorai.002G081900' => 'gra', 'Gorai.007G314800' => 'gra', 'Gorai.009G176000' => 'gra', 'Gorai.011G172500' => 'gra', 'Gorai.013G164100' => 'gra', 'GSVIVG01007339001' => 'vvi', 'GSVIVG01014589001' => 'vvi', 'GSVIVG01027766001' => 'vvi', 'GSVIVG01030640001' => 'vvi', 'GSVIVG01036202001' => 'vvi', 'GSVIVG01036203001' => 'vvi', 'HanXRQChr03g0092041' => 'han', 'HanXRQChr05g0130741' => 'han', 'HanXRQChr08g0233941' => 'han', 'HanXRQChr11g0333051' => 'han', 'HanXRQChr13g0419011' => 'han', 'HanXRQChr13g0422161' => 'han', 'HanXRQChr13g0422191' => 'han', 'HanXRQChr13g0422251' => 'han', 'HanXRQChr13g0422271' => 'han', 'HanXRQChr13g0422421' => 'han', 'HanXRQChr16g0516351' => 'han', 'HanXRQChr17g0551191' => 'han', 'HanXRQChr17g0552431' => 'han', 'Haze_06690' => 'cav', 'Haze_09594' => 'cav', 'Haze_11342' => 'cav', 'Haze_11344' => 'cav', 'Hma1.2p1_0267F.1_g107380' => 'hma', 'Hma1.2p1_0613F.1_g189340' => 'hma', 'Hma1.2p1_0731F.1_g209945' => 'hma', 'Hma1.2p1_1054F.1_g252450' => 'hma', 'Hma1.2p1_1130F.1_g259940' => 'hma', 'Hma1.2p1_1682F.1_g297350' => 'hma', 'Hma1.2p1_2644F.1_g325940' => 'hma', 'Hma1.2p1_2810F.1_g328880' => 'hma', 'HPP92_002203' => 'vpl', 'HPP92_002492' => 'vpl', 'HPP92_002543' => 'vpl', 'HPP92_026547' => 'vpl', 'Hund02140' => 'sun', 'Hund03033' => 'sun', 'Hund06935' => 'sun', 'Hund11876' => 'sun', 'Hund23318' => 'sun', 'Hund23531' => 'sun', 'Lalb_Chr01g0006121' => 'lal', 'Lalb_Chr03g0037171' => 'lal', 'Lalb_Chr14g0366061' => 'lal', 'Lalb_Chr14g0375651' => 'lal', 'Lalb_Chr19g0134721' => 'lal', 'Lalb_Chr22g0357081' => 'lal', 'Lj1A755T26' => 'lonja', 'Lj1A863G59' => 'lonja', 'Lj3g0008180' => 'lja', 'Lj3g0008754' => 'lja', 'Lj3g0024962' => 'lja', 'Lj6A662T58' => 'lonja', 'Lj6g0008025' => 'lja', 'Lj6g0019583' => 'lja', 'Lj8C165T10' => 'lonja', 'Lsat_1_v5_gn_4_57480' => 'lsa', 'Lsat_1_v5_gn_5_5640' => 'lsa', 'Lsat_1_v5_gn_6_92040' => 'lsa', 'Lsat_1_v5_gn_7_108260' => 'lsa', 'Lsat_1_v5_gn_7_108280' => 'lsa', 'Lsat_1_v5_gn_7_18241' => 'lsa', 'Lsat_1_v5_gn_8_129501' => 'lsa', 'Manes.03G122100' => 'mes', 'Manes.03G165600' => 'mes', 'Manes.15G039300' => 'mes', 'Manes.15G077000' => 'mes', 'Manes.16G017300' => 'mes', 'Mapoly0040s0112' => 'mpo', 'MBI02_g29698_MAGBIO' => 'mbi', 'MBI03_g05113_MAGBIO' => 'mbi', 'MBI18_g15335_MAGBIO' => 'mbi', 'MD03G1212600' => 'mdo', 'MD05G1336500' => 'mdo', 'MD05G1336600' => 'mdo', 'MD10G1312000' => 'mdo', 'MD10G1312100' => 'mdo', 'MD11G1227800' => 'mdo', 'MD13G1212400' => 'mdo', 'MD16G1216000' => 'mdo', 'Medtr1g043430' => 'mtr', 'Medtr2g082640' => 'mtr', 'Medtr2g089000' => 'mtr', 'Medtr4g081370' => 'mtr', 'MELO3C002507.2' => 'cme', 'MELO3C006435.2' => 'cme', 'MELO3C018123.2' => 'cme', 'MELO3C018125.2' => 'cme', 'MELO3C019226.2' => 'cme', 'Migut.G00474' => 'egut', 'Migut.H01862' => 'egut', 'Migut.M01814' => 'egut', 'Migut.N00259' => 'egut', 'MSTRG.12953' => 'ama', 'MSTRG.14412' => 'ama', 'MSTRG.24689' => 'ama', 'MSTRG.4125' => 'ama', 'MSTRG.6888' => 'ama', 'MSTRG.9903' => 'ama', 'Nitab4.5_0000342g0020' => 'nta', 'Nitab4.5_0000397g0120' => 'nta', 'Nitab4.5_0002229g0100' => 'nta', 'Nitab4.5_0002238g0060' => 'nta', 'Nitab4.5_0002342g0110' => 'nta', 'Nitab4.5_0002345g0050' => 'nta', 'Nitab4.5_0002916g0050' => 'nta', 'Nitab4.5_0002949g0080' => 'nta', 'Nitab4.5_0003897g0030' => 'nta', 'Nitab4.5_0004036g0020' => 'nta', 'Nitab4.5_0009680g0030' => 'nta', 'Nn1g02721' => 'nnu', 'Nn1g03709' => 'nnu', 'Nn1g06963' => 'nnu', 'Nn2g11259' => 'nnu', 'Nn2g13190' => 'nnu', 'Nn2g13348' => 'nnu', 'Nn3g19623' => 'nnu', 'Nn4g23936' => 'nnu', 'Nn4g26549' => 'nnu', 'Nn5g30023' => 'nnu', 'Nn5g30097' => 'nnu', 'Oeu007618.1' => 'oeu', 'Oeu011077.2' => 'oeu', 'Oeu011993.1' => 'oeu', 'Oeu021413.1' => 'oeu', 'Oeu021429.1' => 'oeu', 'Oeu042911.1' => 'oeu', 'Oeu051231.1' => 'oeu', 'Oeu062621.1' => 'oeu', 'Oeu063892.2' => 'oeu', 'Os02g0116600' => 'osa', 'Os05g0455400' => 'osa', 'Os07g0543000' => 'osa', 'Os08g0138500' => 'osa', 'Peaxi162Scf00007g01347' => 'pax', 'Peaxi162Scf00024g02317' => 'pax', 'Peaxi162Scf00082g01311' => 'pax', 'Peaxi162Scf01086g00136' => 'pax', 'Peaxi162Scf01434g00017' => 'pax', 'PGR031G1009' => 'pgr', 'PGR031G1449' => 'pgr', 'PGR031G3255' => 'pgr', 'PGR042G2770' => 'pgr', 'PGR083G1547' => 'pgr', 'PGR142G3074' => 'pgr', 'PGSC0003DMG400014432' => 'stu', 'PGSC0003DMG400017181' => 'stu', 'PGSC0003DMG400019263' => 'stu', 'PGSC0003DMG400021717' => 'stu', 'PGSC0003DMG400026168' => 'stu', 'Phvul.005G091000' => 'pvu', 'Phvul.005G112500' => 'pvu', 'Phvul.006G196600' => 'pvu', 'Phvul.007G272600' => 'pvu', 'Phvul.011G141300' => 'pvu', 'Potri.001G416600' => 'ptr', 'Potri.004G031800' => 'ptr', 'Potri.008G165700' => 'ptr', 'Potri.010G072900' => 'ptr', 'Potri.011G031000' => 'ptr', 'Potri.011G132400' => 'ptr', 'Pp3c12_4630' => 'ppa', 'Pp3c13_2780' => 'ppa', 'Pp3c4_16270' => 'ppa', 'Pp3c5_28980' => 'ppa', 'Prupe.1G037400' => 'ppe', 'Prupe.4G029000' => 'ppe', 'Prupe.4G201500' => 'ppe', 'Psat5g249760' => 'psa', 'Psat5g266480' => 'psa', 'Psat6g137520' => 'psa', 'Psat7g122200' => 'psa', 'PSO063G6708' => 'pso', 'PSO170G4988' => 'pso', 'PSO210G0150' => 'pso', 'PSO210G3261' => 'pso', 'PSO541G6507' => 'pso', 'PSO675G1528' => 'pso', 'PSO832G2067' => 'pso', 'PSO832G2163' => 'pso', 'QL05p077128' => 'qlo', 'QL06p016979' => 'qlo', 'QL08p013457' => 'qlo', 'QL08p013775' => 'qlo', 'QL08p033978' => 'qlo', 'QL93p0073_1215' => 'qlo', 'RcHm_v2.0_Chr4g0387861' => 'rch', 'RcHm_v2.0_Chr4g0392401' => 'rch', 'RcHm_v2.0_Chr5g0004471' => 'rch', 'RcHm_v2.0_Chr5g0037201' => 'rch', 'Rhsim02G0036000' => 'rsi', 'Rhsim04G0057000' => 'rsi', 'Rhsim06G0156800' => 'rsi', 'Rhsim13G0162200' => 'rsi', 'RhsimUnG0253400' => 'rsi', 'Sabra04G0018100' => 'sbr', 'Sabra08G0126200' => 'sbr', 'Sabra10G0035400' => 'sbr', 'Sabra11G0018500' => 'sbr', 'Sabra11G0024400' => 'sbr', 'Sabra11G0119200' => 'sbr', 'Sabra16G0283200' => 'sbr', 'SalBow2G2117' => 'sbo', 'SalBow3G2213' => 'sbo', 'SalBow7G1848' => 'sbo', 'Sc03g0009150' => 'sci', 'Sc13g0005230' => 'sci', 'Sc13g0005990' => 'sci', 'Sc16g0006560' => 'sci', 'Sed0001786' => 'sed', 'Sed0003408' => 'sed', 'Sed0005486' => 'sed', 'Sed0008257' => 'sed', 'Sed0024068' => 'sed', 'SGA_v2.0_scaffold308G48089' => 'sas', 'SGA_v2.0_scaffold416G51222' => 'sas', 'SGA_v2.0_scaffold67G22772' => 'sas', 'SGA_v2.0_scaffold89G27439' => 'sas', 'SHI31874' => 'shi', 'SHI31875' => 'shi', 'SMO356G0708' => 'smo', 'SMO361G0349' => 'smo', 'SMO361G0585' => 'smo', 'Solyc02g079970.4' => 'sly', 'Solyc07g052670.3' => 'sly', 'Solyc07g064040.3' => 'sly', 'Solyc09g089870.3' => 'sly', 'Solyc10g006510.3' => 'sly', 'Sopen02g024720' => 'spe', 'Sopen07g026270' => 'spe', 'Sopen07g032180' => 'spe', 'Sopen09g032810' => 'spe', 'Sopen10g002460' => 'spe', 'Sp1g37790' => 'spa', 'Sp3g20860' => 'spa', 'Sp6g16640' => 'spa', 'Sp7g12480' => 'spa', 'TAR362G0297' => 'tar', 'TAR369G0819' => 'tar', 'TAR369G0871' => 'tar', 'TAR623G1782' => 'tar', 'TAR624G1103' => 'tar', 'TAR627G0771' => 'tar', 'TAR629G1325' => 'tar', 'TAR633G1048' => 'tar', 'THA.LOC104808617' => 'tha', 'THA.LOC104813411' => 'tha', 'THA.LOC104816916' => 'tha', 'Thecc.02G163000' => 'tca', 'Thecc.04G253100' => 'tca', 'Thecc.06G208800' => 'tca', 'Thecc.07G054900' => 'tca', 'Thhalv10011752m.g' => 'esa', 'Thhalv10014564m.g' => 'esa', 'Thhalv10021177m.g' => 'esa', 'Thhalv10025927m.g' => 'esa', 'TPR.G15864' => 'tpr', 'TPR.G25926' => 'tpr', 'TPR.G30800' => 'tpr', 'TPR.G36845' => 'tpr', 'TWI18G1031' => 'twi', 'TWI38G0644' => 'twi', 'TWI38G1309' => 'twi', 'TWI38G1383' => 'twi', 'TWI39G0997' => 'twi', 'TWI73G1160' => 'twi', 'unitig_21.g20006' => 'ugi', 'unitig_32.g10837' => 'ugi', 'unitig_578.g16763' => 'ugi', 'unitig_748.g8312' => 'ugi', 'vmacro03736' => 'vma', 'vmacro09322' => 'vma', 'vmacro09749' => 'vma', 'vmacro11770' => 'vma', 'vmacro12237' => 'vma', 'vmacro15430' => 'vma', 'VMungo0540G1518' => 'vmu', 'VMungo0720G1381' => 'vmu', 'VMungo1080G0913' => 'vmu', 'VMungo1080G1665' => 'vmu', 'VMungo1127G1348' => 'vmu', 'Zm00001eb006060' => 'zma', 'Zm00001eb171220' => 'zma', 'Zm00001eb173070' => 'zma', 'Zm00001eb209480' => 'zma', 'Zm00001eb229950' => 'zma', 'Zm00001eb289490' => 'zma', 'Zm00001eb323440' => 'zma', 'Zm00001eb383710' => 'zma', 'Zm00001eb386850' => 'zma', 'Zm00001eb416800' => 'zma' ) $gf_id = 'HOM05D001139' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001139' ) $data_identifier = 'HOM05D001139' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 6, 'aag' => (int) 2, 'ach' => (int) 9, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 2, 'arhy' => (int) 10, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 6, 'cqu' => (int) 9, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 4, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 3, 'ccl' => (int) 4, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 7, 'dca' => (int) 8, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 11, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 4, 'hma' => (int) 8, 'vpl' => (int) 4, 'sun' => (int) 6, 'lal' => (int) 6, 'lonja' => (int) 4, 'lja' => (int) 5, 'lsa' => (int) 7, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mdo' => (int) 8, 'mtr' => (int) 4, 'cme' => (int) 5, 'egut' => (int) 4, 'ama' => (int) 6, 'nta' => (int) 11, 'nnu' => (int) 11, 'oeu' => (int) 9, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 5, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 7, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 4, 'tar' => (int) 8, 'tha' => (int) 3, 'tca' => (int) 4, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 6, 'vmu' => (int) 5, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb416800' $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